Interpretive Summary: Like most widely cultivated crops, soybean has a relatively narrow genetic base, while its wild perennial relatives are more genetically diverse and can display desirable traits not present in cultivated soybean. For example, no sources of complete resistance to Sclerotinia stem rot have been identified in soybean. However, high levels of resistance have been observed in some accessions of a wild perennial relative of soybean Glycine latifolia. To identify chromosomal regions associated with resistance to Sclerotinia stem rot, accessions of G. latifolia resistant or sensitive to Sclerotinia stem rot were used to produce mapping populations and identify molecular markers that could be used for gene mapping and identification. Using high-throughput sequencing of G. latifolia DNAs, over 350,000 molecular markers were identified. An average of 456 G. latifolia molecular markers were associated with each of the 20 soybean chromosomes. A subset of the markers mapped in similar orders in soybean and G. latifolia. These results confirmed that the identified molecular markers from G. latifolia will be useful for gene mapping and comparing gene locations between soybean and G. latifolia for the identification and eventual movement of agronomically important genes into soybean. The results will be of interest to scientists who are interested in utilizing the genes from genetically diverse wild soybean species for soybean improvement.

Technical Abstract:
Background: Like most widely cultivated crops, soybean (Glycine max) has a relatively narrow genetic base, while its wild perennial relatives are more genetically diverse and can display desirable traits not present in cultivated soybean. For example, no sources of complete resistance to Sclerotinia stem rot have been identified in soybean. However, high levels of resistance have been observed in some accessions of perennial Glycine species, including G. latifolia. To identify chromosomal regions associated with resistance, accessions of G. latifolia resistant or sensitive to Sclerotinia stem rot were used to produce mapping populations and detect single nucleotide sequence polymorphism (SNP) markers. Results: Reduced representation libraries were prepared from genomic DNAs of G. latifolia accessions PI559298 (resistant) and PI559300 (susceptible), and sequenced on an Illumina sequencer, which produced over 35 million 100-nt reads from each line, about 5% of which aligned to the soybean genome in gene-rich regions on the distal arms of the soybean chromosomes. Few sequences aligned in pericentromeric regions or transposable elements resident in the G. max genome. Comparisons of sequences reads from the two accessions identified over 350,000 SNPs. An average of 456 G. latifolia SNP-containing sequences aligned to each of the G. max chromosomes. To test the usefulness of the SNPs and the synteny between the G. latifolia and G. max genomes, nine SNPs were selected that aligned to soybean chromosome 4 or 13. All nine SNP markers segregated in the expected 1:2:1 ratios in a G. latifolia F2 population, formed two distinct linkage groups, and mapped in similar orders in G. latifolia and G. max. Conclusion: These results confirmed that the SNPs identified from the genome sequences of the two G. latifolia accessions will be useful for gene mapping and comparing gene locations between G. latifolia and G. max for the identification and eventual movement of agronomically important genes into G. max. The lack of sequence conservation in pericentromeric regions may at partially explain the difficulties of producing fertile hybrid plants between G. max and perennial Glycine species.